org.geworkbench.bison.datastructure.bioobjects.microarray
Class CSMarkerValue

java.lang.Object
  extended by org.geworkbench.bison.datastructure.bioobjects.microarray.CSMarkerValue
All Implemented Interfaces:
java.io.Serializable, java.lang.Comparable<DSMarkerValue>, DSMarkerValue, DSMutableMarkerValue
Direct Known Subclasses:
CSExpressionMarkerValue, CSGenepixMarkerValue

public abstract class CSMarkerValue
extends java.lang.Object
implements DSMutableMarkerValue

Title: Plug And Play Framework

Description: Architecture for enGenious Plug&Play

Copyright: Copyright (c) 2002

Company: First Genetic Trust

Version:
$Id: CSMarkerValue.java 7572 2011-03-12 15:27:59Z zji $
Author:
Andrea Califano
See Also:
Serialized Form

Field Summary
protected  float confidence
          Positive values are normal, negative values are masked.
protected static float m_threshold
           
protected static float MISSING
          Value which is assigned to the field confidence to indicate that the marker value is marked as "missing".
protected static float p_threshold
          Used to define how present/marginal/absent calls should be made based on the call p-value: p-value < p_threshold --> Present p_threshold <= p-values < m_threshold --> Marginal p-value >= m_threshold --> Absent
protected  float value
           
 
Constructor Summary
CSMarkerValue()
          Default Constructor
CSMarkerValue(CSMarkerValue m)
           
 
Method Summary
 boolean equals(java.lang.Object obj)
          Compares two expression markers
 double getConfidence()
          A value indicating our confidence in the measured signal.
 char getStatusAsChar()
           
 double getValue()
          Return the signal measurement for this spot.
 boolean isAbsent()
           
 boolean isMarginal()
           
 boolean isMasked()
          This method returns whether this marker should be temporarily ignored by analytical tools
 boolean isMissing()
          Check if the mesurement for this spot is classified as "missing".
 boolean isPresent()
           
 boolean isValid()
          This method returns whether the marker is both unmasked and not undefined.
 void mask()
          Sets the mask bit to be temporarily ignored by analyses methods
 void setAbsent()
           
 void setConfidence(double c)
          Set the confidence level.
 void setMarginal()
           
 void setMarginalThreshold(double mThreshold)
          Set the cutoff p-value used for a Marginal call
 void setMissing(boolean flag)
          Set the status of this spot measurement.
 void setPresent()
           
 void setPresentThreshold(double pThreshold)
          Set the cutoff p-value used for a Present call
 void setValue(double s)
          Set the spot's value.
 void unmask()
          Resets the mask bit to be used by analyses methods
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 
Methods inherited from interface org.geworkbench.bison.datastructure.bioobjects.microarray.DSMarkerValue
deepCopy, getDimensionality
 
Methods inherited from interface java.lang.Comparable
compareTo
 

Field Detail

p_threshold

protected static float p_threshold
Used to define how present/marginal/absent calls should be made based on the call p-value: p-value < p_threshold --> Present p_threshold <= p-values < m_threshold --> Marginal p-value >= m_threshold --> Absent


m_threshold

protected static float m_threshold

MISSING

protected static final float MISSING
Value which is assigned to the field confidence to indicate that the marker value is marked as "missing".

See Also:
Constant Field Values

value

protected float value

confidence

protected float confidence
Positive values are normal, negative values are masked. MISSING indicates missing value.

Constructor Detail

CSMarkerValue

public CSMarkerValue()
Default Constructor


CSMarkerValue

public CSMarkerValue(CSMarkerValue m)
Method Detail

getValue

public double getValue()
Description copied from interface: DSMarkerValue
Return the signal measurement for this spot. For 2-channel data, this is usually the ratio of the 2 channels.

Specified by:
getValue in interface DSMarkerValue
Returns:
marker value

setValue

public void setValue(double s)
Description copied from interface: DSMutableMarkerValue
Set the spot's value.

Specified by:
setValue in interface DSMutableMarkerValue
Parameters:
s - the spot's value

setMissing

public void setMissing(boolean flag)
Description copied from interface: DSMutableMarkerValue
Set the status of this spot measurement. The measurement could be be any spot specific information. eg: Missing, Present, Valid and/or others

Specified by:
setMissing in interface DSMutableMarkerValue

setAbsent

public void setAbsent()

setPresent

public void setPresent()

setMarginal

public void setMarginal()

isValid

public boolean isValid()
Description copied from interface: DSMarkerValue
This method returns whether the marker is both unmasked and not undefined. As a result, there is no corresponding setValid method. Should likely be moved to MarkerValue

Specified by:
isValid in interface DSMarkerValue
Returns:

isAbsent

public boolean isAbsent()

isMarginal

public boolean isMarginal()

isPresent

public boolean isPresent()

isMissing

public boolean isMissing()
Description copied from interface: DSMarkerValue
Check if the mesurement for this spot is classified as "missing".

Specified by:
isMissing in interface DSMarkerValue
Returns:
presence

isMasked

public boolean isMasked()
Description copied from interface: DSMarkerValue
This method returns whether this marker should be temporarily ignored by analytical tools

Specified by:
isMasked in interface DSMarkerValue
Returns:

mask

public void mask()
Description copied from interface: DSMutableMarkerValue
Sets the mask bit to be temporarily ignored by analyses methods

Specified by:
mask in interface DSMutableMarkerValue

unmask

public void unmask()
Description copied from interface: DSMutableMarkerValue
Resets the mask bit to be used by analyses methods

Specified by:
unmask in interface DSMutableMarkerValue

getStatusAsChar

public char getStatusAsChar()

getConfidence

public double getConfidence()
Description copied from interface: DSMarkerValue
A value indicating our confidence in the measured signal.

Specified by:
getConfidence in interface DSMarkerValue
Returns:
confidence

setConfidence

public void setConfidence(double c)
Description copied from interface: DSMutableMarkerValue
Set the confidence level.

Specified by:
setConfidence in interface DSMutableMarkerValue
Parameters:
c - confidence of spot's measument

setPresentThreshold

public void setPresentThreshold(double pThreshold)
Set the cutoff p-value used for a Present call

Parameters:
pThreshold -

setMarginalThreshold

public void setMarginalThreshold(double mThreshold)
Set the cutoff p-value used for a Marginal call

Parameters:
mThreshold -

equals

public boolean equals(java.lang.Object obj)
Compares two expression markers

Specified by:
equals in interface DSMarkerValue
Overrides:
equals in class java.lang.Object
Parameters:
m - MarkerValue marker to be compared to
Returns:
boolean equality